This paper reports an improved bonding method using the IPA (isopropyl alcohol) assisted low-temperature bonding process for the PMMA (polymethylmethacrylate) micro CE (capillary electrophoresis) chip. There is a problem about channel deformations during the conventional processes such as thermal bonding and solvent bonding methods. The bonding test using an IPA showed good results without channel deformations over 4 inch PMMA wafer at $60^{circ}C$ and 1.3 bar for 10 minutes. The mechanism of IPA bonding was attributed to the formation of a small amount of vaporized acetone made from the oxidized IPA which allows to solvent bonding. To verify the usefulness of the IPA assisted low-temperature bonding process, the PMMA micro CE chip which had a $45{mu}m$ channel height was fabricated by hot embossing process. A functional test of the fabricated CE chip was demonstrated by the separation of fluorescein and dichlorofluorescein. Any leakage of liquids was not observed during the test and the electropherogram result was successfully achieved. An IPA assisted low-temperature bonding process could be an easy and effective way to fabricate the PMMA micro CE chip and would help to increase the yield.